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Sample GSM252345 Query DataSets for GSM252345
Status Public on Dec 01, 2008
Title Human Prostate 689
Sample type RNA
 
Channel 1
Source name Reference
Organism Homo sapiens
Characteristics Reference
Extracted molecule total RNA
Extraction protocol Prostate samples embedded in OCT were used for laser capture microdissection (LCM) by the laboratory of Martin Gleave. Total RNA was isolated from microdissected cells using the Arcturus Picopure™ Kit, and the samples were treated with DNAse using the Qiagen RNase-Free DNase Set (Qiagen Inc, Valencia, CA). Total RNA was subjected to two rounds of linear amplification using the Ambion MessageAmpII Kit (Ambion Inc, Austin, TX), quantitated in a Gene-Spec III spectrophotometer (Hitachi, Tokyo) and aRNA integrity evaluated using gel electrophoresis.
Label Cy5
Label protocol Complementary DNA (cDNA) probe pairs were prepared by amino-allyl reverse transcription using 2 µg of amplified RNA from microdissected samples and 30 µg of total RNA from a reference RNA pool composed of total RNA isolated from the LNCap, DU145, and PC3 prostate cell lines. Probes were labeled with either Cy5 or Cy3 fluors (Amersham Bioscience, Piscataway, NJ) and competitively hybridized to custom cDNA microarrays spotted in duplicate with approximately 6,700 unique cDNA clones from the Prostate Expression Database (PEDB) as previously described in Pritchard CC, Hsu L, Delrow J, and Nelson PS. Project normal: defining normal variance in mouse gene expression. Proc Natl Acad Sci U S A 2001;98:13266-13271.
 
Channel 2
Source name Human Prostate 689 treated with Neoadjuvant hormone suppression for 6 mo
Organism Homo sapiens
Characteristics Human Prostate 689. #: 689; Treatment: Neoadjuvant hormone suppression for 6 mo; Reference: HGSv5;
Extracted molecule total RNA
Extraction protocol Prostate samples embedded in OCT were used for laser capture microdissection (LCM) by the laboratory of Martin Gleave. Total RNA was isolated from microdissected cells using the Arcturus Picopure™ Kit, and the samples were treated with DNAse using the Qiagen RNase-Free DNase Set (Qiagen Inc, Valencia, CA). Total RNA was subjected to two rounds of linear amplification using the Ambion MessageAmpII Kit (Ambion Inc, Austin, TX), quantitated in a Gene-Spec III spectrophotometer (Hitachi, Tokyo) and aRNA integrity evaluated using gel electrophoresis.
Label Cy3
Label protocol Complementary DNA (cDNA) probe pairs were prepared by amino-allyl reverse transcription using 2 µg of amplified RNA from microdissected samples and 30 µg of total RNA from a reference RNA pool composed of total RNA isolated from the LNCap, DU145, and PC3 prostate cell lines. Probes were labeled with either Cy5 or Cy3 fluors (Amersham Bioscience, Piscataway, NJ) and competitively hybridized to custom cDNA microarrays spotted in duplicate with approximately 6,700 unique cDNA clones from the Prostate Expression Database (PEDB) as previously described in Pritchard CC, Hsu L, Delrow J, and Nelson PS. Project normal: defining normal variance in mouse gene expression. Proc Natl Acad Sci U S A 2001;98:13266-13271.
 
 
Hybridization protocol Probes were labeled with either Cy5 or Cy3 fluors (Amersham Bioscience, Piscataway, NJ) and competitively hybridized to custom cDNA microarrays spotted in duplicate with approximately 6,700 unique cDNA clones from the Prostate Expression Database (PEDB) as previously described in Nelson PS, Pritchard C, Abbott D, and Clegg N. The human (PEDB) and mouse (mPEDB) Prostate Expression Databases. Nucleic Acids Res 2002;30:218-220 and Pritchard CC, Hsu L, Delrow J, and Nelson PS. Project normal: defining normal variance in mouse gene expression. Proc Natl Acad Sci U S A 2001;98:13266-13271.
Scan protocol Fluorescence array images were collected using a GenePix 4000B fluorescent scanner (Axon Instruments, Foster City, CA) and processed as we have previously described in True L, Coleman I, Hawley S, et al. A molecular correlate to the Gleason grading system for prostate adenocarcinoma. Proc Natl Acad Sci U S A 2006;103:10991-10996.
Description Human Prostate 689 from Human hybridized against Reference
Data processing Changes in gene expression were evaluated using the Statistical Analysis of Microarray (SAM) program (http://www-stat.stanford.edu/_tibs/SAM/) to perform a one-sample t-test assessing the effect of Acyline treatment on gene expression (22). An FDR (false discovery rate) of less than 5% was considered significant. Quantile normalization was performed in Bioconductor (23) to allow single channel comparison of the absolute signal intensities in the experimental channel across different arrays in the same experiment.
 
Submission date Dec 19, 2007
Last update date Dec 28, 2007
Contact name Denise Mauldin
E-mail(s) [email protected]
Phone 2066673480
Fax 2066672917
URL http://www.pedb.org
Organization name Fred Hutchinson Cancer Research Center
Department Human Biology
Lab Peter Nelson
Street address 1100 Fairview Ave N D4-100
City Seattle
State/province WA
ZIP/Postal code 98109
Country USA
 
Platform ID GPL4768
Series (1)
GSE9983 Prostate Cancer Gene Expression Changes with Neoadjuvant Hormone Therapy

Data table header descriptions
ID_REF the unique identifier of the feature derived from the Array List (up to 40 characters long, contained in quotation marks).
VALUE normalized log (experiment/reference) ratio data comparable across rows and samples
MetaCol Column referring to overall organization
MetaRow Row referring to overall organization
Column the column number of the feature.
Row the row number of the feature.
Name the name of the feature derived from the Array List (up to 40 characters long, contained in quotation marks).
X the X-coordinate in µm of the center of the feature-indicator associated with the feature, where (0,0) is the top left of the image.
Y the Y-coordinate in µm of the center of the feature-indicator associated with the feature, where (0,0) is the top left of the image.
Dia. the diameter in µm of the feature-indicator.
F635 Median median feature pixel intensity at wavelength #1 (635 nm).
F635 Mean mean feature pixel intensity at wavelength #1 (635 nm).
F635 SD the standard deviation of the feature pixel intensity at wavelength #1 (635 nm).
F635 CV the coefficient of variation of feature pixel intensity.
B635 the actual background value used for the feature in GenePix Pro calculations (as opposed to B635 Median, for example, which is the local median background.) This column is required because GenePix Pro 5.0 has global and negative control background subtraction methods. If you choose a non-local method, B635 is different to B635 Median
B635 Median the median feature background intensity at wavelength #1 (635 nm).
B635 Mean the mean feature background intensity at wavelength #1 (635 nm).
B635 SD the standard deviation of the feature background intensity at wavelength #1 (635 nm).
B635 CV the coefficient of variation of background pixel intensity.
% > B635+1SD the percentage of feature pixels with intensities more than one standard deviation above the background pixel intensity, at wavelength #1 (635 nm).
% > B635+2SD the percentage of feature pixels with intensities more than two standard deviations above the background pixel intensity, at wavelength #1 (635 nm).
F635 % Sat. the percentage of feature pixels at wavelength 635 that are saturated.
F532 Median median feature pixel intensity at wavelength #2 (532 nm).
F532 Mean mean feature pixel intensity at wavelength #2 (532 nm).
F532 SD the standard deviation of the feature intensity at wavelength #2 (532 nm).
F532 CV the coefficient of variation of feature pixel intensity.
B532 the actual background value used for the feature in GenePix Pro calculations (as opposed to B532 Median, for example, which is the local median background.) This column is required because GenePix Pro 5.0 has global and negative control background subtraction methods. If you choose a non-local method, B532 is different to B532 Median.
B532 Median the median feature background intensity at wavelength #2 (532 nm).
B532 Mean the mean feature background intensity at wavelength #2 (532 nm).
B532 SD the standard deviation of the feature background intensity at wavelength #2 (532 nm).
B532 CV the coefficient of variation of background pixel intensity.
% > B532+1SD the percentage of feature pixels with intensities more than one standard deviation above the background pixel intensity, at wavelength #2 (532 nm).
% > B532+2SD the percentage of feature pixels with intensities more than two standard deviations above the background pixel intensity, at wavelength #2 (532 nm).
F532 % Sat. the percentage of feature pixels at wavelength 532 that are saturated.
Ratio of Medians (635/532) the ratio of the median intensities of each feature for each wavelength, with the median background subtracted.
Ratio of Means (635/532) the ratio of the arithmetic mean intensities of each feature for each wavelength, with the median background subtracted.
Median of Ratios (635/532) the median of pixel-by-pixel ratios of pixel intensities, with the median background subtracted.
Mean of Ratios (635/532) the geometric mean of the pixel-by-pixel ratios of pixel intensities, with the median background subtracted.
Ratios SD (635/532) the geometric standard deviation of the pixel intensity ratios.
Rgn Ratio (635/532) the regression ratio of every pixel in a 2-feature-diameter circle around the center of the feature.
Rgn R2 (635/532) the coefficient of determination for the current regression value.
F Pixels the total number of feature pixels.
B Pixels the total number of background pixels.
Circularity a measure of circularity from 0 to 100, using a metric based on the variance of the distance of each boundary pixel to the centroid of the feature: 100 is most circular, 0 is most non-circular. Circular features always have a circularity of 100, square features always have a circularity of 79 (
Sum of Medians (635/532) the sum of the median intensities for each wavelength, with the median background subtracted.
Sum of Means (635/532) the sum of the arithmetic mean intensities for each wavelength, with the median background subtracted.
Log Ratio (635/532) log (base 2) transform of the ratio of the medians.
F635 Median - B635 the median feature pixel intensity at 635 with the median background subtracted.
F532 Median - B532 the median feature pixel intensity at 532 with the median background subtracted.
F635 Mean - B635 the mean feature pixel intensity at 635 with the median background subtracted.
F532 Mean - B532 the mean feature pixel intensity at 532 with the median background subtracted.
F635 Total Intensity the sum of all pixel intensities in the feature at wavelenth 635.
F532 Total Intensity the sum of all pixel intensities in the feature at wavelenth 532.
SNR 635 the signal-to-noise ratio of the feature, calculated as (F635 Mean - B635 Mean)/B635 SD.
SNR 532 the signal-to-noise ratio of the feature, calculated as (F532 Mean - B532 Mean)/B532 SD.
Flags the type of flag associated with a feature.
Normalize the normalization status of the feature (included/not included).
Autoflag reports whether or not a feature has been flagged from the Flag Features dialog box. It applies to good and bad flags only.

Data table
ID_REF VALUE MetaCol MetaRow Column Row Name X Y Dia. F635 Median F635 Mean F635 SD F635 CV B635 B635 Median B635 Mean B635 SD B635 CV % > B635+1SD % > B635+2SD F635 % Sat. F532 Median F532 Mean F532 SD F532 CV B532 B532 Median B532 Mean B532 SD B532 CV % > B532+1SD % > B532+2SD F532 % Sat. Ratio of Medians (635/532) Ratio of Means (635/532) Median of Ratios (635/532) Mean of Ratios (635/532) Ratios SD (635/532) Rgn Ratio (635/532) Rgn R2 (635/532) F Pixels B Pixels Circularity Sum of Medians (635/532) Sum of Means (635/532) Log Ratio (635/532) F635 Median - B635 F532 Median - B532 F635 Mean - B635 F532 Mean - B532 F635 Total Intensity F532 Total Intensity SNR 635 SNR 532 Flags Normalize Autoflag
237241 0.185541696 1 1 1 1 gi|220150|gb|D90427|D90427 3170 9900 110 1145 1183 354 29 446 446 455 124 27 100 95 0 1076 1112 361 32 372 372 377 75 19 100 96 0 0.993 0.996 1.008 1.022 1.874 0.992 0.581 80 517 100 1403 1477 -0.010 699 704 737 740 94648 88936 5.871 9.800 0 0 0
237242 -2.542131325 1 1 2 1 gi|179280|gb|M27132.1|HUMATPSYB 3340 9890 90 18100 19707 7347 37 386 386 468 569 121 100 100 0 3565 3831 1579 41 331 331 347 130 37 100 100 0 5.477 5.520 4.907 5.797 1.785 6.898 0.582 52 370 100 20948 22821 2.453 17714 3234 19321 3500 1024742 199196 33.812 26.800 0 0 0
237243 1 1 3 1 gi|12420723|gb|BG030944|BG030944 3540 9880 140 348 348 83 23 379 379 437 486 111 0 0 0 325 328 55 16 340 340 352 103 29 2 0 0 2.067 2.583 1.450 1.512 3.762 4.361 0.250 156 922 100 -46 -43 1.047 -31 -15 -31 -12 54279 51198 -0.183 -0.233 -50 0 0
237244 -0.944507228 1 1 4 1 gi|21536438|ref|NM_012161.2| 3730 9890 90 1548 4796 10382 216 392 392 446 485 108 96 63 1 950 1263 1459 115 347 347 362 93 25 96 94 0 1.917 4.808 2.072 2.833 3.594 13.057 0.239 52 390 100 1759 5320 0.939 1156 603 4404 916 249413 65659 8.969 9.688 0 0 0
237245 -0.48607151 1 1 5 1 gi|21536438|ref|NM_012161.2| 3940 9900 100 1459 1544 565 36 410 410 422 108 25 100 97 0 1100 1175 345 29 358 358 368 83 22 97 96 0 1.414 1.388 1.396 1.423 2.106 1.499 0.700 80 455 100 1791 1951 0.500 1049 742 1134 817 123523 94013 10.389 9.723 0 0 0
237246 1 1 6 1 gi|14065685|gb|BG755019|BG755019 4120 9880 140 446 536 714 133 452 452 1341 6162 459 0 0 0 368 382 85 22 371 371 427 437 102 0 0 0 2.000 7.636 2.155 2.115 4.653 33.200 0.467 156 804 100 -9 95 1.000 -6 -3 84 11 83626 59579 -0.131 -0.103 -50 0 0
237247 1 1 7 1 gi|15996756|gb|BI856009|BI856009 4320 9880 140 434 481 220 45 464 464 1401 6416 457 0 0 0 373 382 93 24 380 380 433 447 103 0 0 0 4.286 8.500 1.677 1.592 5.112 13.112 0.006 156 733 100 -37 19 2.100 -30 -7 17 2 75021 59539 -0.143 -0.114 -50 0 0
237248 1 1 8 1 gi|19586973|gb|BM969386|BM969386 4510 9870 140 482 489 137 28 494 494 512 139 27 12 3 0 392 394 62 15 393 393 398 70 17 13 2 0 12.000 -5.000 1.850 1.786 3.646 8.420 0.031 156 810 100 -13 -4 3.585 -12 -1 -5 1 76293 61514 -0.165 -0.057 -50 0 0
237249 -1.985133655 1 1 9 1 gi|7703647|gb|AW771590| 4710 9880 100 10591 11544 5485 47 491 491 524 176 33 100 100 0 3238 3649 1504 41 394 394 400 66 16 100 100 0 3.551 3.396 3.222 3.257 1.827 4.612 0.613 80 461 100 12944 14308 1.828 10100 2844 11053 3255 923552 291932 62.614 49.227 0 0 0
237250 1 1 10 1 gi|20408448|gb|BQ227048|BQ227048 4900 9870 140 498 494 116 23 467 467 488 166 34 7 1 0 394 399 60 15 385 385 394 87 22 10 1 0 3.444 1.929 2.352 2.269 3.458 12.734 0.020 156 834 100 40 41 1.784 31 9 27 14 77123 62257 0.036 0.057 -50 0 0
237251 0.654644414 1 1 11 1 gi|11012215|gb|AU150694|AU150694 5080 9870 110 1689 1800 773 42 467 467 507 227 44 98 91 0 2729 2921 1214 41 388 388 427 374 87 98 98 0 0.522 0.526 0.507 0.493 2.078 0.665 0.563 80 519 100 3563 3866 -0.938 1222 2341 1333 2533 144017 233645 5.696 6.668 0 0 0
237252 1 1 12 1 gi|17298590|gb|AC009167.8| 5290 9870 140 429 445 120 26 457 457 488 193 39 5 0 0 373 397 181 45 380 380 407 293 71 2 0 0 4.000 -0.706 1.500 1.791 4.060 0.067 0.015 156 876 100 -35 5 2.000 -28 -7 -12 17 69421 61890 -0.223 -0.034 -50 0 0
237253 -0.835016674 1 1 13 1 gi|13477360|gb|BC005157|BC005157 5480 9880 110 1024 1163 576 49 428 428 437 116 26 100 98 0 601 618 150 24 364 364 381 256 67 48 5 0 2.515 2.894 2.578 2.966 2.177 2.302 0.091 80 521 100 833 989 1.330 596 237 735 254 93017 49431 6.259 0.926 0 0 0
237254 1 1 14 1 UNKNOWN_4 5680 9870 140 376 381 96 25 397 397 409 125 30 5 1 0 342 351 99 28 350 350 365 207 56 0 0 0 2.625 -16.000 1.759 1.601 4.099 3.091 0.016 156 831 100 -29 -15 1.392 -21 -8 -16 1 59427 54828 -0.224 -0.068 -50 0 0
237255 1 1 15 1 gi|5031976|ref|NM_005746.1| 5880 9870 140 376 386 104 26 389 389 400 125 31 10 1 0 345 349 59 16 346 346 379 326 86 0 0 0 13.000 -1.000 1.912 1.680 4.835 8.596 0.003 156 769 100 -14 0 3.700 -13 -1 -3 3 60273 54464 -0.112 -0.092 -50 0 0
237256 1 1 16 1 gi|4827043|ref|NM_005121.1| 6070 9870 140 445 445 114 25 420 420 433 116 26 19 2 0 358 370 97 26 358 358 367 80 21 9 2 0 100000.000 2.083 2.077 2.280 5.130 131.267 0.000 156 726 100 25 37 16.610 25 0 25 12 69394 57779 0.103 0.038 -50 0 0
237257 1 1 17 1 BLANK 6260 9870 140 399 413 102 24 420 420 427 111 25 14 1 0 360 379 208 54 359 359 367 67 18 16 1 0 -21.000 -0.350 1.948 2.014 4.584 0.059 0.000 156 754 100 -20 13 Error -21 1 -7 20 64406 59107 -0.126 0.179 -50 0 0
237258 1 1 18 1 UNKNOWN_6 6460 9870 140 372 382 109 28 389 389 428 352 82 0 0 0 341 343 83 24 352 352 409 727 177 0 0 0 1.545 0.778 2.093 2.086 3.719 0.421 0.611 156 792 100 -28 -16 0.628 -17 -11 -7 -9 59617 53446 -0.131 -0.091 -50 0 0
237259 -0.156363248 1 1 19 1 gi|14042897|gb|AK027893|AK027893 6650 9890 120 2931 3144 1245 39 438 438 497 449 90 99 97 0 3197 3412 1540 45 371 371 457 875 191 93 85 0 0.882 0.890 0.907 0.944 1.910 0.616 0.547 120 556 100 5319 5747 -0.181 2493 2826 2706 3041 377312 409389 5.895 3.377 0 0 0
237260 1 1 20 1 gi|5901981|ref|NM_006899.1| 6850 9870 140 518 538 129 23 508 508 542 308 56 1 0 0 401 407 81 19 400 400 410 152 37 1 0 0 10.000 4.286 1.672 1.581 5.362 3.271 0.299 156 819 100 11 37 3.322 10 1 30 7 83876 63518 -0.013 -0.020 -50 0 0

Total number of rows: 15488

Table truncated, full table size 4217 Kbytes.




Supplementary file Size Download File type/resource
GSM252345.gpr.gz 1.6 Mb (ftp)(http) GPR
Processed data included within Sample table
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